Data Quality Assessment Report

massqc from tidymass by Xiaotao Shen

2022-02-18


INTRODUCTION

massqc (version 0.01): Created in 2021 by Xiaotao Shen


PARAMETERS

Table 1: Parameter setting

pacakge_name function_name parameter time
massprocesser process_data path:mzxml_ms1_data/NEG 2022-02-18 23:24:35
massprocesser process_data polarity:negative 2022-02-18 23:24:35
massprocesser process_data ppm:10 2022-02-18 23:24:35
massprocesser process_data peakwidth:10,60 2022-02-18 23:24:35
massprocesser process_data snthresh:10 2022-02-18 23:24:35
massprocesser process_data prefilter:3,500 2022-02-18 23:24:35
massprocesser process_data fitgauss:FALSE 2022-02-18 23:24:35
massprocesser process_data integrate:2 2022-02-18 23:24:35
massprocesser process_data mzdiff:0.01 2022-02-18 23:24:35
massprocesser process_data noise:500 2022-02-18 23:24:35
massprocesser process_data threads:4 2022-02-18 23:24:35
massprocesser process_data binSize:0.025 2022-02-18 23:24:35
massprocesser process_data bw:5 2022-02-18 23:24:35
massprocesser process_data output_tic:FALSE 2022-02-18 23:24:35
massprocesser process_data output_bpc:FALSE 2022-02-18 23:24:35
massprocesser process_data output_rt_correction_plot:FALSE 2022-02-18 23:24:35
massprocesser process_data min_fraction:0.5 2022-02-18 23:24:35
massprocesser process_data fill_peaks:FALSE 2022-02-18 23:24:35
massdataset create_mass_dataset() no:no 2022-02-18 23:24:52
massdataset mutate() parameter_1:batch=as.character(batch) 2022-02-18 23:35:31

SAMPLE INFORMATION

#> -------------------- 
#> massdataset version: 0.99.7 
#> -------------------- 
#> 1.expression_data:[ 8804 x 259 data.frame]
#> 2.sample_info:[ 259 x 6 data.frame]
#> 3.variable_info:[ 8804 x 3 data.frame]
#> 4.sample_info_note:[ 6 x 2 data.frame]
#> 5.variable_info_note:[ 3 x 2 data.frame]
#> 6.ms2_data:[ 0 variables x 0 MS2 spectra]
#> -------------------- 
#> Processing information (extract_process_info())
#> create_mass_dataset ---------- 
#> process_data ---------- 
#> mutate ----------

Figure 1: Peak intensity profile.


MISSING VALUES


MISSING VALUES IN DATASET

Black is MV.

Figure 2: Missing values in dataset


MISSING VALUES IN VARIABLES

Figure 3: Missing values in variables


MISSING VALUES IN SAMPLES

Figure 4: Missing values in samples


RSD DISTRIBUTATION

Figure 5: RSD distributation


INTENSITY FOR ALL THE VARIABLES

Figure 6: Intensity for all the variables


SAMPLE CORRELATION

Figure 7: Sample correlation


PCA score plot

Figure 7: PCA score plot